De Novo Assembly Methods for Next Generation Sequencing Data  

作　　者：Yiming He Zhen Zhang Xiaoqing Peng Fangxiang Wu Jianxin Wang 

机构地区：[1]the School of Information Science and Engineering, Central South University [2]the Morehouse School of Medicine [3]the Department of Mechanical Engineering and Division of Biomedical Engineering, University of Saskatchewan

出　　处：《Tsinghua Science and Technology》2013年第5期500-514,共15页清华大学学报（自然科学版（英文版）

基　　金：supported in part by the National Natural Science Foundation of China (Nos.61232001,61128006,and 61073036)

摘　　要：The recent breakthroughs in next-generation sequencing technologies, such as those of Roche 454,Illumina/Solexa, and ABI SOLID, have dramatically reduced the cost of producing short reads of the genome of new species. The huge volume of reads, along with short read length, high coverage, and sequencing errors, poses a great challenge to de novo genome assembly. However, the paired-end information provides a new solution to these problems. In this paper, we review and compare some current assembly tools, including Newbler, CAP3, Velvet,SOAPdenovo, AllPaths, Abyss, IDBA, PE-Assembly, and Telescoper. In general, we compare the seed extension and graph-based methods that use the overlap/lapout/consensus approach and the de Bruijn graph approach for assembly. At the end of the paper, we summarize these methods and discuss the future directions of genome assembly.The recent breakthroughs in next-generation sequencing technologies, such as those of Roche 454,Illumina/Solexa, and ABI SOLID, have dramatically reduced the cost of producing short reads of the genome of new species. The huge volume of reads, along with short read length, high coverage, and sequencing errors, poses a great challenge to de novo genome assembly. However, the paired-end information provides a new solution to these problems. In this paper, we review and compare some current assembly tools, including Newbler, CAP3, Velvet,SOAPdenovo, AllPaths, Abyss, IDBA, PE-Assembly, and Telescoper. In general, we compare the seed extension and graph-based methods that use the overlap/lapout/consensus approach and the de Bruijn graph approach for assembly. At the end of the paper, we summarize these methods and discuss the future directions of genome assembly.

关 键 词：next-generation sequencing genome assembly overlap/lapout/consensus de Bruijn graph 

分 类 号：Q78[生物学—分子生物学]